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Progress of Joint Research Activities

Research No. 1: TC Model Joint Research (Agriculture-1) Date: Oct. 20 , 2019
th
1 General Title Exploitating, conservating and sustainable use of rice genetic resources in
Mekong Delta on adaptation to climate change

2 Core Members CTU: Le Viet Dung (Project Leader), Huynh Quang Tin, Nguyen Thanh Tam, Tran Xuan Phuc, Vo Cong
Thanh, Tran Thi Phuong Thao, Nguyen Loc Hien, Huynh Ky, Tran Nhan Dung, Nguyen Thi Pha, Nguyen
Tri Yen Nhi
Japanese Universities and Companies: KISHIMA Yuji (Hokkaido University)
3 Duration Aug. 2016 – Aug. 2018 (2 years)
4 Main Objectives - To evaluate the agro-morphological characteristics and salinity tolerance of local rice varieties.
- To study on the diversity of genetic source of 99 local and improved rice varieties.
- To determine genetic diversity of OsHKT1,5 gene from 44 rice varieties
- To assess genetic diversity of 44 Vietnam local rice varieties by SSR marker assisted with salt tolerance
5 Focal Points AGRO-MORPHOLOGICAL DIVERSITY OF RICE Pearson correlation among salinity tolerance related traits
GENETIC RESOURCE TO SALINITY TOLERANCE SES20 SES20 1 PHA 1 RLA SW RW PHD RLD SWD RWD
PHA
-.340 **
RLA -.680 ** .461 ** 1
SW -.812 ** .598 ** .684 ** 1
- 97 out of collected 485 rice accessions were tested and PHD RW -.766 ** .569 ** .711 ** -.603 ** -.577 ** 1 1
.941 **
-.421 **
.425 **
-.824 **
screened for salinity tolerance. There were 4 salinity- RLD SWD .711 ** -.368 ** -.887 ** -.698 ** -.693 ** .433 ** .649 ** 1 1
-.860 **
-.833 **
.600 **
.782 **
-.596 **
-.422 **
tolerant accessions (SES score ≤3), 36 accessions got SES RWD .708 ** -.443 ** -.612 ** -.825 ** -.887 ** .592 ** .663 ** .924 ** 1
score from 3-5. SES20: standard evaluation score at 20 days after treated; PHA: plant height after
treated; RLA: root length after treated; SW: shoot weight after treated; RW: root
- 43 rice varieties were evaluated salinity tolerance in Ca weight after treated; PHD: plant height deduction; RLD: root length deduction; SWD:
shoot weight deduction; RWD: root weight deduction; **significant at P < 0.001
Mau province resulting in 13 good tolerance (score 3).
- Determination of mineral (Na, K, Mg, Ca)
concentration in root, leaf and stem was different
among varieties and the negative correlation between
Na + concentration in leaf and the ratio of dry weight
between salt treatments and control was main finding.
- SES score at 20 days after treated to salt condition was
positive correlation with Na, Ca concentration and Na/K Reduction of mineral uptake in salt condition (%). (A):
ratio, but there was no correlation with K concentration. general reduced percentage between salt treatment and Field experiments at salinity
control treatment of Na, K, Ca, Mg (%); (B): detail
information of reduced percentage between salt treatment area of Ca Mau province (2017)
and control treatment of Na, K, Ca, Mg (%).
SNPs IDENTIFICATION FROM NGS SEQUENCING TO SALINITY TOLERANCE IN RICE LANDRACES
Population structure of 99 MDR rice
a. Sites b. accessions cultivated in coastal of
492
601 Mekong delta of Vietnam (the red
500
435 node indicated japonica, the blue
556 node indicated indica group)
536
751
680
699
1011
962
991
Characteristic of SNP c.
a. SNP distribution along the entire
in 12 chromosomes of 100 rice SNP location in rice genomes Phylogenetic analysis of
Splices site
genome. Promoter 0% Intron OsHKT 1,5 protein fragment
23%
b. Distances between SNP in 100 Intergenic Coding 20% 3'-UTR 3% 5'-UTR 2% of 44 rice varieties
38%
rice genome. 14%
c. Localization of SNPs in whole
genome levels Splices site Intron 5'-UTR 3'-UTR Coding Intergenic Promoter
Polymorphism among 44 Vietnam local rice
varieties by using 20 SSR markers m1 m2 m4
GENETIC DIVERSITY OF LOCAL RICE (Oryza No. of No. of PIC Annealin Product m11 m13 m21 m23 m19
sativa L.) BY SSR MARKERS No. Markers allele polymorphi value g Temp. size m22 m3 m16 m5
c alleles
s
( o C)
(bp)
- Twenty SSR markers have been used to characterize the 1 RM10694 5 2 0.7014 58 218-235 m6 m20 m7 m25 m28
genetic diversity of 44 local rice varieties of Viet Nam. The 2 3 RM10745 3 1 1 0 0.4918 0 58 58 182-201 m30 m17 m8 m10
RM10748
110
SSR markers located on chromosome 1, 5, 6, 9, 11 of rice 4 RM10793 8 5 0.8091 58 145-210 m10 m29 m26 m27 m12
0.3146
76-92
plant that were choose had linked with salt tolerance. A 5 6 RM10825 2 2 1 1 0.2392 55 58 180-200 m14 m24 m9 m18
RM10843
total of 77 alleles were detected in which 14 SSR markers 7 RM3412 10 7 0.7898 55 207-281 m15 m31 m33 m38
RM7075
located at chromosomes 1. There were 18/20 markers are 8 9 RM8046 6 2 2 0 0.6289 55 58 138-189 m34 m41 m37 m39
0.2044
125-225
polymorphic with an average of 3.85 alleles per marker. 10 11 RM140 3 5 1 2 0.4662 58 58 250-307 m40 m42 m36 m32
102-195
0.7108
RM206
- The result of clustering revealed that the 44 of local rice 12 RM215 2 1 0.0624 55 71-114 m44 m35 m43
RM122
genotypes could broadly be classified into 8 groups at a 13 14 RM253 5 5 2 3 0.595 58 55 228-400 0.57 0.67 Coefficient 0.77 0.88 0.98
199-306
0.6341
truncation level of 0.69 in the coefficient scale. Group I, II 15 RM293 1 0 0 56 170
0.683
comprised only genotypes gave sensitive phenotype and 16 17 RM333 5 4 1 3 0.4018 55 55 166-196
117-146
RM302
group VIII comprised only genotypes gave tolerance 18 RM5461 3 1 0.1754 56 120-191 Cluster analysis of genetic diversity of 44 local
rice in Viet Nam by using 20 SSR markers
RM1287
phenotype. 19 20 RM10684 2 3 1 1 0.0624 55 58 229-237
0.4966
126-161
Mean 3.85 1.75 0.423345
6 Comments All experiments were done. This research still continues towards finalizing papers to submit Journals.
ⓒ All Rights Reserved, Dec. 2019 (CTU)
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